Brad et al,

I would like second the issue you raise so succinctly. The failure to automatically track the original sample name throughout the analysis (that and  array selection of paired end reads) is one of the biggest barriers people face for doing work on many samples in galaxy. It just gets very confusing unless you spend a lot of time workarounds (creating workflows to rename things, editing datasets individually, etc) – especially for non-programmer users, for whom workflows with variables and API calls are beyond the pale.

Regards,

Curtis

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Langhorst, Brad
Sent: Thursday, November 13, 2014 3:23 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

I think adding the available inputs is a good improvement - I know it will save me some mistakes.

I think I might have been unclear in my comment ("single least intuitive part")... I'm not referring to how input name chaining works - I'm talking about the default naming of datasets based on the analysis step and the immediate inputs.

When interpreting results, we care about two things: 

1) which analysis 

2) which sample is being described by that analysis.

The chain of analysis is important, but its easily determined by looking at the info tab, or generating a workflow from the history to the order of events.

The current naming system requires that we walk the entire chain of analysis back to the original dataset, or laboriously build every workflow to manually carry the sample information along in the input and output naming.

If the default display convention showed the original dataset dataset name, much of that toting of input name could be avoided.

Maybe I'll find some time to implement this someday...

Brad

---

From: Dannon Baker <dannon.baker@gmail.com>
Sent: Thursday, November 13, 2014 10:05 AM
To: Langhorst, Brad
Cc: Jan Hapala; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

Hi all,

For these parameters, 'input' refers to the exact tool input name.   Recent versions of Galaxy will now tell you what the options are to use, like the following I see for bowtie2:

I definitely agree that it's not intuitive, and I'm trying to think of ways to make this better -- suggestions definitely welcome.

-Dannon

On Wed, Nov 12, 2014 at 6:54 AM, Langhorst, Brad <Langhorst@neb.com> wrote:

Hi Jan:

Are you using input dataset tool? I'm not sure it's required - but I habitually use it.

I'm attaching an image of a working renaming setup. I hope it helps.

brad

---

From: Jan Hapala <jan@hapala.cz>
Sent: Wednesday, November 12, 2014 9:29 AM
To: Langhorst, Brad
Subject: Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

Thanks, Brad. This is informative, but I'm still stuck.

I have an input dataset which passes data to FASTQ Summary Statistics. (I have tried other tools, as well.)

The output file name is: stats on: #{input1}

The name of the Input dataset is: input1

I get this result: stats on:

Jan

2014-11-12 14:06 GMT+01:00 Langhorst, Brad <Langhorst@neb.com>:

For what it's worth (not much ;), I think the dataset naming is the single least intuitive part of the galaxy system for biologists.

I think there's a proposal to "fix" this problem - and mainain the connection between input data set and derived data, but It doesn't seem to have gone anywhere yet. 

Anyway, you have to check the name of the field for each tool - it's sometimes "input" and sometimes something else.

You want to use the #{} for naming.  The ${} stuff is for parameters

I also do this kind of thing: to keep the names from getting too long.

#{input_1 | basename}.bam

The basename removes everything after the last . character.

Brad

---

From: galaxy-dev-bounces@lists.bx.psu.edu <galaxy-dev-bounces@lists.bx.psu.edu> on behalf of Jan Hapala <jan@hapala.cz>
Sent: Wednesday, November 12, 2014 7:49 AM
To: galaxy-dev
Subject: [galaxy-dev] rename output dataset in workflow - input dataset variable

Hello,

I want to rename ouput datasets in a workflow in such a way that the name contains the name of the input dataset. I could not find instructions in the manual (and this info is missing in the Workflow editor - would be really helpful there!).

I tried #{input}, e.g. "stats on: #{input}" (with no quotes), but I keep getting just "stats on:" The variable is empty. When I use ${input}, I get a variable field in the workflow form (I do not want this).

My G. instance: Galaxy changeset: d1e1beeb532239250396dd8fbdc0156508c6744e

Can anyone help me, please?

Jan

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